{"id":"W4404902753","doi":"10.1186/s13059-024-03441-1","title":"SMART: spatial transcriptomics deconvolution using marker-gene-assisted topic model","year":2024,"lang":"en","type":"article","venue":"Genome biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; St. Paul's Hospital; University of British Columbia Hospital","funders":"","keywords":"Deconvolution; Biology; Computational biology; Context (archaeology); Identification (biology); Transcriptome; Gene; Cell type; Gene expression; Genetics; Cell; Computer science; Algorithm","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001877987,0.001102007,0.001185026,0.0006618223,0.0004009635,0.0009594932,0.001545332,0.001257847,0.001539198],"category_scores_gemma":[0.00291919,0.0005535028,0.001683563,0.001015616,0.0006716234,0.001325941,0.001539015,0.001643313,0.001018349],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007097567,"about_ca_system_score_gemma":0.001584273,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003808262,"about_ca_topic_score_gemma":0.006619885,"domain_scores_codex":[0.9995459,0.0001363577,0.00001706776,0.0001518926,0.0001133896,0.0000353756],"domain_scores_gemma":[0.9991568,0.000478732,0.00007548304,0.0001391954,0.0001052304,0.00004458841],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0009070107,0.0001929791,0.005035231,0.000483839,0.00072018,0.0003662553,0.0003263174,0.581247,0.1280037,0.03439921,0.01350844,0.2348098],"study_design_scores_gemma":[0.0000226242,0.00002076193,0.0004482603,0.000004440205,0.00001849401,0.00004357005,0.00001114333,0.9818626,0.007117463,0.008368026,0.002058089,0.00002464059],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.009223113,0.0001927127,0.9873446,0.0001248561,0.00002334295,0.00002459019,0.0004704242,0.002250841,0.0003455372],"genre_scores_gemma":[0.2189408,0.0006237319,0.7697091,0.0003750901,0.0001308666,0.0003531596,0.004460922,0.001460348,0.003945888],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003808262,"threshold_uncertainty_score":0.009931922,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03064309977635044,"score_gpt":0.2615926337446557,"score_spread":0.2309495339683053,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}